Background: The profitability of the beef industry is directly influenced by the fertility rate and reproductive performance of both males and females, which can be improved through selective breeding. When performing genomic analyses, genetic markers located on the X chromosome have been commonly ignored despite the X chromosome being one of the largest chromosomes in the cattle genome. Therefore, the primary objectives of this study were to: (1) estimate variance components and genetic parameters for eighteen male and five female fertility and reproductive traits in Nellore cattle including X chromosome markers in the analyses; and (2) perform genome-wide association studies and functional genomic analyses to better understand the genetic background of male and female fertility and reproductive performance traits in Nellore cattle. Results: The percentage of the total direct heritability (h²_total) explained by the X chromosome markers (h²_x) ranged from 3 to 32% (average: 16.4%) and from 9 to 67% (average: 25.61%) for female reproductive performance and male fertility traits, respectively. Among the traits related to breeding soundness evaluation, the overall bull and semen evaluation and semen quality traits accounted for the highest proportion of h²_x relative to h²_total with an average of 39.5% and 38.75%, respectively. The total number of significant genomic markers per trait ranged from 7 (seminal vesicle width) to 43 (total major defects). The number of significant markers located on the X chromosome ranged from zero to five. A total of 683, 252, 694, 382, 61, and 77 genes overlapped with the genomic regions identified for traits related to female reproductive performance, semen quality, semen morphology, semen defects, overall bulls’ fertility evaluation, and overall semen evaluation traits, respectively. The key candidate genes located on the X chromosome are PRR32, STK26, TMSB4X, TLR7, PRPS2, SMS, SMARCA1, UTP14A, and BCORL1. The main gene ontology terms identified are “Oocyte Meiosis”, “Progesterone Mediated Oocyte Maturation”, “Thermogenesis”, “Sperm Flagellum”, and “Innate Immune Response”. Conclusions: Our findings indicate the key role of genes located on the X chromosome on the phenotypic variability of male and female reproduction and fertility traits in Nellore cattle. Breeding programs aiming to improve these traits should consider adding the information from X chromosome markers in their genomic analyses.

We explored the influence of maternal nutritional strategies on the development of the rumen and cecum in offspring. Additionally, we investigated the potential repercussions of prenatal nutrition on the rumen and fecal microbiota composition, utilizing metagenomic 16S techniques, to understand the effects of fetal programming (FP) in Nellore cattle. A total of 63 bulls submitted to different prenatal nutrition strategies, namely, non-programming (NP), partial programming (PP), and complete programming (CP), were evaluated. The rumen epithelium was methodically evaluated based on the presence of rumenitis and structural irregularities. The assessment of cecum lesions was conducted post-evisceration, whereby all thoroughly cleaned ceca were methodically evaluated. Samples from 15 animals of rumen fluid at slaughter and feces during the finishing phase were collected, respectively. All DNA extraction were carried out using the Macherey Nagel NucleoSpin Tissue^®, and 16S sequencing was conducted using the V4 primers on the MiSeq platform. Within the ruminal ecosystem, an estimated range of 90 to 130 distinct amplicon sequence variants was discerned, as distributed across 45,000 to 70,000 sequencing reads. Our metagenomic exploration unveils microbial communities that distinctly mirror gastrointestinal tract microenvironments and dietary influences. In sum, this comprehensive study advances our comprehension of FP, highlighting the interplay of maternal nutrition, gastrointestinal development, and microbial communities, contributing significantly to the fields of animal science.

The Suffolk is a meat-type sheep that is the predominant terminal-sire breed in the U.S. Known for its rapid growth, high carcass yield, and efficient feed conversion, Suffolk rams are crucial in commercial crossbreeding systems. Despite its importance, the parameters used by the National Sheep Improvement Program (NSIP) in its genetic evaluation have not been updated in over two decades. Therefore, we re-estimated genetic and phenotypic parameters and calculated theoretical accuracies and genetic trends for various growth, body composition, and reproductive traits in U.S. Suffolk sheep. The traits evaluated were birth weight (BWT), weaning weight (WWT), post-weaning weight (PWWT), post-weaning eye muscle depth (EMD), post-weaning fat depth (CFAT), and number of lambs born (NLB) and weaned (NLW) per ewe lambing. The dataset consisted of a pedigree comprising 70,271 individuals and up to 48,000 phenotypic records per trait across more than 100 flocks. Variance components were estimated using the Restricted Maximum Likelihood method and animal models with maternal and permanent environmental effects fitted when appropriate. Records were pre-adjusted for age at recording, birth type, rearing type, and dam age as relevant. For lamb traits, contemporary group (CG; concatenation of flock, birth year, management group, sex, lambing interval, and recording date, except for BWT) was the only fixed effect included in the models. For reproductive traits, CG combined flock and lambing year; ewe age was added as a categorical fixed effect. Heritability estimates (±SE) ranged from 0.04 ± 0.008 for NLW to 0.24 ± 0.025 for CFAT. Maternal heritabilities ranged from 0.02 ± 0.01 for PWWT to 0.16 ± 0.011 for BWT. Genetic correlations among growth traits ranged from 0.47 ± 0.07 to 0.67 ± 0.04, and genetic correlations between PWWT and body composition traits were positive (0.30 ± 0.09 with EMD and 0.55 ± 0.08 with CFAT). A strong genetic correlation (0.81 ± 0.03) was observed between NLB and NLW. Theoretical accuracy was highest for proven animals with progeny records. Genetic trends showed progress in growth and muscling traits but declining maternal breeding values for growth traits. Several updated genetic parameters diverged from legacy NSIP estimates, likely due to shifts in management and trait definitions. These results emphasize the need for regular re-estimation of genetic parameters to ensure accurate genetic evaluations and promote balanced genetic progress across traits.

This study evaluated the influence of variance component (VC) estimates, obtained from different models and two relationship matrices, pedigree‐based (BLUP) and genomic information‐based (ssGBLUP), on genomic predictions of carcass traits in Montana composite cattle. Phenotypic records from 14,422 animals were analysed for ribeye area, rump fat thickness, backfat thickness and marbling, along with pedigree information from 193,129 animals and genomic data from 3911 animals genotyped with 49,457 SNPs. Variance components and heritability estimates were calculated using restricted maximum likelihood under single‐trait linear models. Across five models (M1–M5), fixed effects included contemporary group, embryo transfer, age at ultrasound and cow age at calving, while random effects included direct genetic effect and residual. From model M2 onwards, biological type, heterosis and both combined and specific recombination effects were also considered. The Akaike information criterion (AIC) was used to identify the best‐fitting model. Different VC estimates were applied in ssGBLUP predictions to evaluate predictive ability based on accuracy, bias and dispersion. Variance component and heritability estimates were similar between methods, although ssGBLUP yielded higher direct additive genetic variances and heritabilities. More parameterised models using ssGBLUP provided a better fit according to AIC. However, less parameterised models showed superior predictive ability, regardless of whether VCs were estimated by BLUP or ssGBLUP. When comparing predictive ability across sources, pedigree‐based VC estimates resulted in more accurate predictions. Thus, the choice of model complexity should be guided by the analysis objective and the available data structure.

Background and Aim: Canine otitis externa is a common inflammatory disorder in which bacterial and yeast proliferation may complicate treatment and contribute to recurrence. In Brazil, limited information is available comparing recurrent and non-recurrent cases while simultaneously characterizing microbial isolates and their antimicrobial susceptibility. This study compared clinical, otoscopic, and cytological findings between recurrent and non-recurrent otitis externa, identified bacterial and yeast isolates, evaluated their in vitro susceptibility to selected fluoroquinolones and antifungal agents, and investigated associations between clinical and microbiological variables and recurrence. Materials and Methods: Fifty-seven dogs with otitis externa presented to a veterinary hospital in Brazil were evaluated by otoscopy and cytology. Ear secretions were cultured, and isolates were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Antimicrobial susceptibility was evaluated by disk diffusion. Clinical and cytological findings were compared between recurrent and non-recurrent cases, and associations with disease status were assessed using Fisher's exact test and log-linear Poisson regression. Results: Cytology demonstrated bacterial proliferation in 54/57 (94.7%) and yeast proliferation in 25/57 (43.9%) samples. Microbial growth occurred in 46/57 (80.7%) samples, yielding 40 identified bacterial isolates and 16 Malassezia pachydermatis isolates. Staphylococcus was the predominant bacterial genus (21/40; 52.5%), and Staphylococcus pseudintermedius was the most frequent species (10/40; 25.0%). Resistance to both ciprofloxacin and enrofloxacin occurred in 37.5% of bacterial isolates. Among M. pachydermatis isolates, resistance occurred to fluconazole (43.8%), nystatin (31.3%), amphotericin B (12.5%), and ketoconazole (6.3%), whereas no isolate was resistant to miconazole. Recurrence was not significantly associated with the evaluated clinical or microbiological variables, although antifungal-resistant M. pachydermatis showed a nonsignificant trend toward association with recurrent disease. Cytological bacterial proliferation showed the strongest association with higher expected frequencies (RR = 18.0, p < 0.001). Conclusion: S. pseudintermedius and M. pachydermatis were the most common microorganisms recovered from canine otitis externa. The substantial fluoroquinolone resistance among bacterial isolates supports culture and susceptibility testing rather than empirical therapy. Variable antifungal resistance among M. pachydermatis isolates, particularly in recurrent cases, warrants further investigation. These findings provide baseline data for antimicrobial surveillance and stewardship in canine otitis externa in Brazil. Keywords: antifungal resistance, antimicrobial resistance, Brazil, canine otitis externa, fluoroquinolones, Malassezia pachydermatis, microbial culture, Staphylococcus pseudintermedius.

This study investigated the effects of maternal nutrition on hepatic long non-coding RNA (lncRNA) expression in Nellore cattle offspring. To this end, a total of 126 pregnant cows were assigned to three dietary treatments: not programmed (mineral supplementation only), partial programming (late protein-energy supplementation), and full programming (protein-energy supplementation throughout pregnancy). At 676±28 days of age, liver samples were collected from the offspring to perform RNA-sequencing. Novel lncRNAs were identified with FEELnc and CPC2, and differentially expressed lncRNAs (DELs) with DESeq2. Partial correlation, information theory, and regulatory impact factor were used to identify key regulatory roles, while over-representation analysis was performed to detect enriched processes. Among the 3,257 lncRNAs identified, 17 were DELs (false discovery rate<0.1). The PPxNP comparison exhibited the highest transcriptional changes (10 DELs), including IncRNA TU7296, identified as a potential regulator of energy metabolism and immune function, as well as molecular functions associated with oxidative metabolism. The FPxNP comparison revealed distinct regulation of genes related to fatty acid transport and oxidative protein folding. The FPxPP comparison showed minimal differences, highlighting the similarity between these groups. This study provides insights into the role of maternal nutrition in modulating long-term epigenetic programming via lncRNA-mediated mechanisms in beef cattle offspring.